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Ground-penetrating radar (GPR) provides high-resolution imaging for shallow archaeological prospection, but its effectiveness is greatly reduced in the conductive, clay-rich alluvium of southwestern Taiwan—especially when exploring Neolithic cultural layers with low electrical impedance contrast between the archaeological targets and surrounding sediments. To overcome this challenge, we conducted an integrated geophysical study at the eastern sector of the Sanmin Road Neolithic site in Tainan, Taiwan. Our approach combines GPR attribute analysis, microtremor analysis, and electrical/gamma-ray borehole logging to understand subsurface stratigraphy and delineate the geometry of the potential cultural horizon. The survey investigated a channel–floodplain transitional environment hosting a Mid-Neolithic cultural layer (ca. 4,000 BP). We observed a strong link between GPR attributes—particularly energy and similarity—and Horizontal-to-Vertical Spectral Ratio (HVSR) resonance peaks, both in depth and lateral continuity of the horizon. Borehole data validated these findings, with core lithology and recovered pottery sherd confirming the stratigraphic and cultural context. The mapped horizon shallows toward the northeast and correspondingly deepens toward the northwest, with subbottom depths between 4.5 to 6.0 meters, and some localized anomalies immediately above this horizon may indicate recent human activities. By combining multiple geophysical methods, our results characterize the geometry, physical properties, and stratigraphy of the interpreted cultural layer. This integrated geophysical framework substantially improves the reliability of studying cultural layers under challenging geological settings, providing a solid basis for planning heritage excavation, preservation, and management.